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- PDB-7uzp: parathyroid hormone 1 receptor extracellular domain complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7uzp
Titleparathyroid hormone 1 receptor extracellular domain complexed with a peptide ligand containing three beta-amino acids
Components
  • PTHrP[1-36] 24,28,31 XCP
  • Parathyroid hormone/parathyroid hormone-related peptide receptor
KeywordsSIGNALING PROTEIN / parathyroid hormone 1 receptor / signaling / beta-amino acid
Function / homology
Function and homology information


parathyroid hormone receptor activity / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / bone mineralization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / peptide hormone binding / chondrocyte differentiation / cell maturation ...parathyroid hormone receptor activity / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / bone mineralization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / peptide hormone binding / chondrocyte differentiation / cell maturation / bone resorption / skeletal system development / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / : / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / basolateral plasma membrane / in utero embryonic development / cell population proliferation / cell surface receptor signaling pathway / receptor complex / apical plasma membrane / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / protein homodimerization activity / nucleus / plasma membrane / cytoplasm
Similarity search - Function
GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like ...GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsYu, Z. / Bruchs, A.T. / Bingman, C.A. / Gellman, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM056414 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Altered signaling at the PTH receptor via modified agonist contacts with the extracellular domain provides a path to prolonged agonism in vivo.
Authors: Liu, S. / Yu, Z. / Daley, E.J. / Bingman, C.A. / Bruchs, A.T. / Gardella, T.J. / Gellman, S.H.
History
DepositionMay 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Feb 28, 2024Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parathyroid hormone/parathyroid hormone-related peptide receptor
B: PTHrP[1-36] 24,28,31 XCP
C: Parathyroid hormone/parathyroid hormone-related peptide receptor
D: PTHrP[1-36] 24,28,31 XCP
E: Parathyroid hormone/parathyroid hormone-related peptide receptor
F: PTHrP[1-36] 24,28,31 XCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5149
Polymers44,3246
Non-polymers1903
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-66 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.650, 58.949, 77.924
Angle α, β, γ (deg.)90.000, 117.570, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Parathyroid hormone/parathyroid hormone-related peptide receptor / PTH/PTHrP type I receptor / PTH/PTHr receptor / Parathyroid hormone 1 receptor / PTH1 receptor


Mass: 11995.670 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTH1R, PTHR, PTHR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03431
#2: Protein/peptide PTHrP[1-36] 24,28,31 XCP


Mass: 2779.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28 % v/v PEG Smear Low, 0.1 M tris-HCl pH 8, 0.15 M Sodium citrate, 1% ethylene glycol, 0.4 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.29→34.54 Å / Num. obs: 18565 / % possible obs: 99.7 % / Redundancy: 7.501 % / Biso Wilson estimate: 41.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.107 / Χ2: 0.873 / Net I/σ(I): 12.62 / Num. measured all: 139252 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.29-2.357.0580.8362.549733138013790.7710.90399.9
2.35-2.417.6050.6533.299864130212970.8450.70199.6
2.41-2.487.6520.573.739993130613060.8910.612100
2.48-2.567.5690.4654.529711129012830.9090.49999.5
2.56-2.647.6280.3775.469093119411920.9490.40499.8
2.64-2.747.6310.2837.18989118011780.9680.30499.8
2.74-2.847.6050.2288.288677114211410.9840.24499.9
2.84-2.967.6550.1849.918459111111050.9890.19899.5
2.96-3.097.610.1312.878044105810570.9940.13999.9
3.09-3.247.6070.11714.5675699959950.9930.126100
3.24-3.417.5780.08717.1572529619570.9970.09499.6
3.41-3.627.6340.07320.3769709149130.9970.07899.9
3.62-3.877.5070.06922.6163218448420.9970.07499.8
3.87-4.187.5140.06423.8960948148110.9970.06999.6
4.18-4.587.4720.06125.2754627387310.9980.06699.1
4.58-5.127.4250.06425.1549976756730.9970.06999.7
5.12-5.917.3750.06925.2644036005970.9960.07499.5
5.91-7.247.1860.07525.635504964940.9970.08199.6
7.24-10.246.940.07726.5527624043980.9960.08398.5
10.24-34.546.060.0824.9613092262160.9930.08795.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
autoPROC1.0.5 (20210420)data reduction
XDSFeb 5, 2021 (BUILT 20210322)data reduction
Aimless0.7.7data scaling
pointless1.12.10data scaling
autoPROC1.0.5 (20210420)data scaling
PHASERphasing
XSCALEJan 10, 2022 BUILT=20220220data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FJ3

6fj3


Resolution: 2.29→34.54 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 960 5.19 %
Rwork0.209 17520 -
obs0.2107 18480 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.55 Å2 / Biso mean: 60.6824 Å2 / Biso min: 22.37 Å2
Refinement stepCycle: final / Resolution: 2.29→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 21 146 3177
Biso mean--67.24 45.65 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.410.36861300.278524842614100
2.41-2.570.26591400.269625162656100
2.57-2.760.29251450.249524512596100
2.76-3.040.29291320.226724832615100
3.04-3.480.25481220.216725402662100
3.48-4.380.2161410.17124922633100
4.39-34.540.20811500.19552554270499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0091-2.0113-4.64255.65761.82677.6532-0.28421.4534-0.7169-0.46820.23290.62070.7383-0.81070.10170.5666-0.1722-0.09170.6386-0.10710.4999-18.868918.28077.2463
27.37190.7982-2.14683.8926-1.16295.85660.0480.9110.04510.1105-0.06920.4992-0.1484-0.81830.07240.3117-0.0837-0.0740.46980.02040.4698-26.273920.793120.8551
39.155-0.4727-4.867.58392.24768.035-0.4429-0.1236-0.5959-0.01680.3242-0.13590.33280.18130.0810.2076-0.0407-0.05630.27990.04440.4298-15.22319.532524.1576
42.45852.1054-3.06536.8098-0.72986.7411-0.74090.7002-1.3032-0.92960.4123-0.59980.19440.74580.44420.4911-0.07850.07510.514-0.21020.5763-2.202222.37310.9729
54.3481-2.1333.68652.4237-1.31814.4591-0.7947-0.9932-0.34950.01120.3191-0.896-0.87830.98610.39590.2829-0.00190.00990.6196-0.07040.5518-10.056626.575325.0203
69.6931-4.57064.62394.2637-5.56867.45940.48910.57-0.4837-2.1033-0.5941-0.84831.11150.73710.2810.72170.08870.13450.5256-0.00590.538317.51419.69557.3468
77.5033-3.13734.90026.0677-3.13713.61780.5523-0.404-0.5798-0.8654-0.36-0.37440.6067-0.0206-0.20580.46530.10060.03850.50390.01620.523519.515312.0320.4831
85.09310.4991-0.96797.2671-4.33857.90660.11470.00130.21980.4385-0.1963-0.546-0.32130.22430.06040.22220.0289-0.06160.2571-0.01570.353514.944322.496324.2136
92.172-1.17781.29369.48160.68872.262-0.30190.61140.1437-1.3940.2694-0.50090.0655-0.5187-0.08040.40190.0232-0.01790.37420.03650.39146.171532.745911.2284
108.5824-4.0031-5.49999.33515.67745.5657-0.31520.06430.74341.71090.43350.26950.3542-1.6174-0.17470.61260.11850.09110.3840.07130.58196.125923.459425.0719
117.18063.84444.71634.55774.51584.7345-0.77840.76661.1145-1.86420.16991.0852-1.00450.53570.53290.8603-0.0468-0.07510.60860.09810.5414-1.375651.34217.4499
126.211.42610.49198.51380.5714.5275-0.67660.11040.7959-0.91780.62080.1111-0.74910.4830.01470.4753-0.0497-0.01610.28330.02010.4483.823256.054620.8808
137.64261.58974.49756.05793.10399.22610.0544-0.28180.3334-0.0586-0.13420.43-0.1147-0.23730.06140.3351-0.01450.02190.1979-0.02060.4293-1.827448.424924.2731
147.5125.10315.38514.92395.03515.14770.3116-1.156-0.61010.2039-0.30351.7770.1265-1.16370.09480.3811-0.107-0.0130.5408-0.02750.603-10.187839.388722.9288
157.94532.4594-1.36022.91662.75725.55360.18190.5539-0.3017-0.7703-0.06650.72470.5341-0.81090.01140.487-0.0177-0.16950.4039-0.02010.4244-6.976834.638211.1726
162.54383.454-2.3286.101-2.71652.37820.5729-0.4039-0.89890.4364-0.15070.54971.4340.7392-0.48480.5714-0.052-0.08670.4208-0.00650.55040.764539.130225.0393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 57 )A30 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 80 )A58 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 130 )A81 - 130
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 29 )B15 - 29
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 36 )B30 - 36
6X-RAY DIFFRACTION6chain 'C' and (resid 30 through 57 )C30 - 57
7X-RAY DIFFRACTION7chain 'C' and (resid 58 through 80 )C58 - 80
8X-RAY DIFFRACTION8chain 'C' and (resid 81 through 130 )C81 - 130
9X-RAY DIFFRACTION9chain 'D' and (resid 15 through 29 )D15 - 29
10X-RAY DIFFRACTION10chain 'D' and (resid 30 through 36 )D30 - 36
11X-RAY DIFFRACTION11chain 'E' and (resid 30 through 57 )E30 - 57
12X-RAY DIFFRACTION12chain 'E' and (resid 58 through 80 )E58 - 80
13X-RAY DIFFRACTION13chain 'E' and (resid 81 through 123 )E81 - 123
14X-RAY DIFFRACTION14chain 'E' and (resid 124 through 130 )E124 - 130
15X-RAY DIFFRACTION15chain 'F' and (resid 16 through 29 )F16 - 29
16X-RAY DIFFRACTION16chain 'F' and (resid 30 through 36 )F30 - 36

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